Contacts of the helix formed by residues 389 - 398 (chain A) in PDB entry 2B9S
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 389 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A CYS* 4.2 4.9 - - - -
388A LEU* 1.3 79.3 - - - +
390A PRO* 1.4 75.6 - - + +
391A THR* 3.1 15.6 + - - +
392A GLN* 2.9 52.6 + - - +
393A LEU* 3.2 9.7 + - - +
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Residues in contact with PRO 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A VAL* 3.9 17.7 - - + +
316A GLY 3.8 22.4 - - - +
317A ASN* 3.4 33.4 - - - +
318A GLU 5.4 2.0 - - - +
330A CYS* 4.0 20.4 - - + -
389A ASN* 1.4 90.2 - - + +
391A THR* 1.3 56.0 + - - +
393A LEU* 3.3 2.5 + - + +
394A ASN* 2.8 40.9 + - - +
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Residues in contact with THR 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389A ASN* 3.1 13.8 + - - +
390A PRO* 1.3 78.5 - - - +
392A GLN* 1.3 62.1 + - + +
394A ASN* 3.9 3.2 - - - +
395A ASP* 3.0 45.8 + - - +
118E T 4.2 21.3 - - - +
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Residues in contact with GLN 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A HIS* 3.3 41.1 + - + +
301A ARG* 4.5 3.5 + - - -
387A GLN 3.5 4.4 + - - +
388A LEU* 3.4 5.7 + - + -
389A ASN* 2.9 46.9 + - - +
391A THR* 1.3 78.7 - - + +
393A LEU* 1.3 63.3 + - - +
395A ASP* 3.5 5.7 + - - +
396A HIS* 3.0 24.8 + - - +
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Residues in contact with LEU 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A ARG* 4.1 19.5 - - + +
304A ALA* 3.7 29.8 - - + -
305A MET* 4.2 15.3 - - + +
308A ILE* 3.8 25.6 - - + -
315A VAL* 4.1 6.5 - - + -
330A CYS* 4.4 4.0 - - - -
388A LEU* 4.0 17.8 - - + +
389A ASN 3.2 10.1 + - - +
390A PRO* 3.3 9.6 + - + +
392A GLN* 1.3 78.7 - - - +
394A ASN* 1.3 61.4 + - - +
396A HIS* 3.4 4.6 + - - +
397A LEU* 3.2 45.9 + - + +
406A ALA* 4.1 9.0 - - + -
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Residues in contact with ASN 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A VAL* 4.6 3.0 - - - +
390A PRO* 2.8 28.2 + - - +
391A THR* 4.2 3.8 - - - +
393A LEU* 1.3 72.4 - - - +
395A ASP* 1.3 65.8 + - - +
397A LEU* 3.5 7.8 + - - +
398A LYS* 3.1 40.4 + - - +
405A SER* 3.2 10.5 - - - -
406A ALA* 2.9 31.6 + - - +
117E C 2.9 39.3 + - - +
118E T 4.3 9.4 - - - +
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Residues in contact with ASP 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A THR* 3.0 35.9 + - - +
392A GLN* 3.8 5.2 - - - +
394A ASN* 1.3 75.2 - - - +
396A HIS* 1.3 66.9 + - - +
398A LYS* 3.2 25.7 + - - +
399A SER* 3.8 3.3 + - - -
118E T 5.0 7.1 + - - -
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Residues in contact with HIS 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A SER* 4.6 3.2 + - - -
290A ASP* 4.3 10.2 + - - -
301A ARG* 3.4 53.0 + - + +
305A MET* 3.9 23.6 - - + +
392A GLN 3.0 18.4 + - - +
393A LEU 3.7 4.3 - - - +
394A ASN 3.4 0.2 - - - -
395A ASP* 1.3 75.3 - - - +
397A LEU* 1.3 57.3 + - + +
399A SER* 2.6 44.2 + - - -
400A PHE* 3.7 24.0 - + - -
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Residues in contact with LEU 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A ILE* 5.0 0.7 - - + -
305A MET* 4.2 31.0 - - + -
308A ILE* 6.2 0.4 - - + -
393A LEU* 3.2 29.1 + - + +
394A ASN* 3.7 16.6 - - - +
395A ASP 3.2 0.4 - - - -
396A HIS* 1.3 71.5 - - + +
398A LYS* 1.3 61.1 + - - +
399A SER 3.1 5.8 - - - -
400A PHE* 3.1 19.7 + - + +
401A MET 3.6 9.2 + - - +
404A LEU* 3.6 28.7 - - + +
405A SER 3.6 31.0 - - - +
406A ALA* 3.7 7.0 - - - +
409A PHE* 4.0 26.7 - - + -
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Residues in contact with LYS 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A ASN* 3.1 21.7 + - - +
395A ASP* 3.2 17.3 + - - +
397A LEU* 1.3 74.8 - - - +
399A SER* 1.3 58.9 + - - +
400A PHE 3.2 0.4 - - - -
401A MET 3.4 16.7 + - - +
402A ASP* 4.4 8.1 - - - +
403A GLY* 3.9 29.2 - - - +
404A LEU 2.6 26.8 + - - +
405A SER* 4.0 3.6 - - - -
118E T 2.9 33.6 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il